From The Beginning
by The Iron Sisters
Summary: A crazy twist on the Mortal Instruments series. I don't own any of these characters.
1. The Beginning

**Jace**

Life here is so unfair. My dad is always running off to do what I don't know. I have a feeling he is telling me the half of it and I'm going to figure out what he's hiding.

 **Clary**

Things are very weird in my life. Every so often my mom takes me to a guy's house. What he does here is weird. I'm strapped to a pole. Then, he shoots blue, yellow, and green sparks out of his strangely big hands. My mom is hiding something and it's up to me to figure out what that is.

 **Jace**

My dad died today. He was murdered right in front of me. The Clave is having me live in the NYC institute because he has some old friends there. I'm looking forward to moving because they have two kids about my age. I'm scared that the men who killed my father are going to come back for me.

 **Clary**

I met a guy named Simon today at school. We both go to a catholic school where all kids look alike. When I first saw him, I knew where we going to be friends. I kind of pitted the guy. He was the new kid just standing there. His glasses were too big for his small face and clashed with his dark brown hair. I have good hopes for our friendship that will come.

 **Jace**

Today is the day I'm leaving for New York and I'm very nervous to travel. This is my first time traveling via portal. As I prepare to travel, I take in everything from my childhood. I don't know when I will return. _Weeks? Months? Years?_ I walk outside and take in the view of the house that I grew up in. I dawdle to the Clave members and warlock that stand in my yard. I take one last look at the house before I turn away, I can't have tears fall. No one can find out how much this hurts me. But it has to be done. I quickly jump into the portal before I lose my courage. Soon, I am standing in front of an abandoned church, the New York Institute, my new home. I quickly shake off the glamour and look at the real building. It loomed before me, towering in stone. It doesn't look like anyone is home but there was one person waiting outside for me.

 **Clary**

I had an amazing day today at school. My friend Simon (Yes, we are now officially friends) asked if he could come over after school. I called my mom and she said yes! All day long I waited in anticipation of this afternoon _. RING!_ Yes! That was the final bell at our school, St. Xaviers. That means Simion and I are free to hang out outside of school. We agreed to meet outside the school and walk to my house together. I raced to our meeting spot and waited for him to appear. I was happy I got outside first because then I could catch my breath.

 **Jace**

I slowly approached the person outside. _Who was he? How do I know that he's not my enemy?_ But when I was close enough he didn't do anything but say, "The name's Alec. I'm guessing you're Jace Wayland. Come with me." Reluctantly I followed him. he went straight into the abandoned church. Why? I don't know. He started drawing a rune on his arm. Then he grabbed my hand. The Institute was not abandoned, for sure. I think it was just a glamour. As we walked around, I got the run down of the place. Then, all of a sudden, this smoking hot babe walks up to Alec and I and said, "You must be Jace. I'm Isabelle , but most people call me Izzy. I'm Alec's not as annoying sister, but if you touch me, I'll kick your butt." I was in shock that a girl said that to me. I mean who is immune to my charm? All of a sudden, a cat appeared. I thought Alec was crazy because he started to talk to the cat, but then the cat started walking and motioned for us to come. We appeared in a large room with people in it. They introduced themselves as Maryse and Robert Lightwood. I stopped listening to them when my dad was brought up. I mean I'm only 10 years old and don't need to be reminded that my dad is dead at the drop of a hat. After a long day, all I wanted to do was go to sleep. I interrupted Maryse when she was talking to ask where my room was. She gave me directions and I went to my room. It felt so good to fall asleep.

 **Clary**

When Simon finally came out of the building, school had been over for 15 minutes and I was itching to go play. The walk to my house was very awkward, we didn't talk at all. I was so happy when we got home because Luke's truck was in the driveway. I raced inside leaving Simon to follow me. It was an awkward introduction between Simon, my mom, and Luke. We raced towards the backyard and played for hours on end. We didn't notice the time flying by until the moon was in the pitch black night sky. We walked inside and found the adults laying on the couch. It was already so late that I begged my mom to let Simon sleepover. She called his mom who reluctantly said yes. She was over in the next 20 minutes and brought his stuff. It was very exciting because it was my first sleepover and it was with a guy. Thinking back, I don't even remembered what we did or what we ate, all I remembered was how much happiness I had with Simion spending the night for the first time.

 _ **Fast forward 6 years to Jace sparing with Alec...**_


	2. The Attack

**Jace**

I looked around, confused. _Where did Alec go?_ He was just in front of me. I wiped the sweat threatening to drip into my eyes. All of a sudden, Alec comes and attacks me from behind. I thought I could beat him. But as usual he is full of surprises. "Focus Jace, mind your surroundings."

"I'm trying."

"Obviously not, usually you would see that coming. What's going on?"

"I don't know. Something's not right."

"We'll, figure it out, it's messing with your head and we have a mission tonight."

"Alright, whatever."

I knew exactly what was up. I saw this girl, but she saw me even when I had a glamour on I think. She was a short but amazingly beautiful redhead. I quickly turned away because I didn't want her to get drawn into my crazy life. She seemed very confused and out of place. I think something was bothering her and it was up to me to find out what was up. If she could see me that meant that she had the Sight.

 **Clary**

Today was weird day. I went to the Pandemonium Club with Simon because I was mad at my mom. When I was there, bumped into me. He was all upset when I said, "You don't need to say sorry." He said, "You can see me?" I ran away quickly because that weirded me out. I mean, of course I can see him, he is a person. I went up to Simon and told him what happened. I pointed to where the guy was and he hadn't moved. Simon said he couldn't see anyone. I thought I was going insane. But there was nothing I could do to convince him. Anyway, I had to leave the mysterious guy because Simon had a gig to get to for his band.

Thinking back, Simon's gig was AWESOME! It was the best they ever had. He slept over again that night. Sleepovers with him are and always will be awesome.

 **Jace**

After a long day of training, it felt good for my mind to be blank on a mission. Alec, Izzy, and I destroyed 20 demons that night. Oh! What fun it is to explore the sewers. Our mission started out differently though. We started out at a club called the Pandemonium Club. That girl that I thought was out of place bumped into me here. That's when I told Alec and Izzy about this girl. I have a feeling we need to keep our eyes on her. She seems different in a way I can't explain. One question though, why is she at the Pandemonium Club? She seems like a mundane. A mundane has no reason to be in a place like this.

 **Clary**

I met the weird dude again. The one that Simon said he couldn't see. I wonder if he's okay because I saw a human being for sure. A very hot a muscular human being. I don't think he is human though. Some sort of species where you look perfect. We met at a little cafe by my house. Erick, one of Simon's weird band mates read poetry and forced us to go. Yet again, I met the mysterious guy. I keep running into him. I should find out why. _Is he following me?_ This is starting to get a little creepy. He appeared in front of me. _How can he run so fast?_ "You can see me right?"

"Yes , I can see you. Am I not supposed to?"

"Not really. You have the Sight. Come with me."

"Why should I trust you?"

"Because I might be your one chance at staying alive."

It was all insane. To make matters worse, I got a call from my mom. This guy could see my annoyed look.

"What's wrong?" He asked.

"It's just that my mom just called me and we are still in the middle of a fight."

"You should talk to her."

"I can't."

"Well, her voice mail said not to come home. I need to check on her."

"Bye, stranger person that I don't know."

"I'll come with you. It could be dangerous at your house."

"Fine." _It's not like he will listen to me anyway._

Slowly we made our way to my house. Halfway there I realized that I had left Simon: so I sent him a quick text explaining the situation. He said it was fine and would take a taxi home. _What would I do without Simon?_ When we were in front of the porch, he abruptly took out a glowing dagger and whispered, "Stay back."

 **Jace**

I could tell this was her first time being this close to danger. I mean her face went slack when I pulled out my seraph blade. As we walked inside, I could smell the demon blood. Her mom must be a Shadowhunter. Only they can injure a demon. Speaking of non-Shadowhunters, the girl was puking in a corner. She said she could smell it too but it only smelled like rot and sewage to her. I raced up the stairs hoping her mom wasn't hurt. But only puddles of ichor spotted the floor. Her mom and the demon have disappeared or so I thought. When Clary walked into the living room, I was still exploring the puddles of ichor.

"Ahhhh!"

I heard a scream come from Clary. When I walked into the living room, I saw was the demon folding in on itself. Her mother was still missing, but Clary was attacked. It only took me a few seconds to kill the demon. She on the other hand, was in very bad condition. I had to take her to the Institute to see Hodge. We had to move fast. She was losing blood and fast. I gave her a quick iratze knowing I will hear crap about it later.

 **Clary**

My body was on fire. Every move I made, pain blinded me.


	3. Who I Am

**So I found a mistake in chapter 2 and I tried to edit it out, the edits are there when I go to change it but they won't save. So Clary and Jace are introduced in this chapter not in chapter 2.**

 **Hope you like it!**

 **Clary**

I feel like crap. I'm waiting in a place called the Institute infirmary. When I wake up, the blondie is looming over me. He calls out to a guy named Hodge who comes sprinting in. I quickly put my head up and immediately regretted it. Pain shot up my back causing a huge wave of pain to wash over me. _What happened? Why am I in so much pain?_ The last thing I remember is this really slimy and creepy looking thing lunging at me, I scream and then the rest is blank. I just woke up here. The Hodge guy is getting closer. I don't even know the name of the blondie that brought me here. _I should find out and thank him._ He looks at me with a worried look. "That's Hodge. He has experience with this kinda stuff and he pretty much safer your life other than the iratze I gave you."

"First of all, I don't even know your name and you gave me a what?!"

"My name is Jace. I don't know your name either and it's called an iratze. A healing rune."

"The name is Clary and what is a rune?"

"I'll explain all of that later. Right now we need to make sure you're okay."

I smiled sheepishly at the fact that he cared that I was hurt. But then a thought occurred to me. _I'm just a random girl. I'm not that important, but Jace acts like it. I talk to him later after he explains all of this._ My thoughts were interrupted when the Hodge guy started talking.

"She'll be okay she's all healed. But Maryse wants to talk to you about the iratze you gave her without even knowing if she was a Shadowhunter or not. She waiting for you in her office."

"See you later Clary, rest up."

He started walking out but then stopped and said, "Ask Hodge to take you to the training room when he's done fixing you up"

"Ok I will"

Soon he was out the door and I didn't see him for a while until I got the training room. He was in all black training with other kid. I didn't want to interrupt them so I just stepped out of sight. For a while, they didn't notice me. Then Jace spotted me.

"Oh hey Clary, how's it going."

"Good. I just walked in and now I'm watching you train. Who's that with you?"

"Oh, now you guys talking about me," the guy said, "The name's Alec. I'm Jace's parabatai."

"What's a parabatai?" I asked because I have no idea what anyone is talking about. "Oh! My name is Clary. Sorry I'm just a little confused Jace still has to explain all of this craziness I got myself into."

"Seriously Jace, you haven't told her yet?!"

"No, I haven't and I was planning to after I finished training."

"Well now she's wondering what you're talking about so make sure you tell her."

"Tell me what?" I asked because I was getting very confused and just wanted to get to the bottom of everything. He stopped dodging Alec's stabs and turned to me. Apparently this is going to be a long talk.

"What you are. You're a Shadowhunter. Half angel and half mundane of human. Shadowhunters hunt demons. What is in my hand is called a seraph blade, made from adamas. Steles are also made from adamas which are used to draw runes. But to be able to hold a seraph blade you need to get the rune of Angelic Power, it looks like this. He showed me a rune on the inside of his wrist. _I've seen that before. But where?_

"Ummm…" Was all I said in reply because I am getting a very big headache from all of this. "I'm going to go lay down." I said as I left the room.

 **Jace**

"Gosh," Alec said, "way to ease into it."

"Well, I'm trying. You try explaining all of them to someone that was a mundane for 16 years."

"Someone is cranky." Alec said as I started out.

He is right, I am a bit cranky because I couldn't sleep. I was up all night thinking about Clary. I feel like she was put in my life for a reason and I'm determined to figure out why that is.


	4. The Twist

**Hellloooooooo! Sorry for the long wait. Schools been insane for us. We only have two days left though so thats good. The only problem is, those two days are final days. Study, study, study! We hope you guys like the new chapter! :)**

 **Clary**

 _Where did I see that "rune"? I remember it from somewhere. What is going on with all this Shadowhunter business?_ Then, a noise interrupted my thoughts. A book has slid under the door along with a note. It said: "If you're confused read this book, It's called the Shadowhunter's' Codex. What's inside should explain everything. -Alec" I checked the hallway to see if he was there but it was empty. _Well, what's the worst that could happen? It's only a book_. I opened the book and started reading. I stopped after a while not knowing how long I was reading but u was almost done with the book. _Well that makes a lot more sense now. I'll have to thank Alec later._ I continued reading and the next thing I know someone is knocking on the door. I open it to find Jace holding a tray piled with food. The sight of it made my stomach growl. He chuckled and said, "Maryse figured that you were busy trying to make sense of all of this so she did to let you skip dinner. She insists that you eat something before you go to bed." I stepped aside to let him in. He set the tray on the bed and surveyed the room. His eyes stopped at the open book on my desk. "Is that the Shadowhunter's Codex?" I nod. "Alec dropped it off and told me that if I read it, it would clear some things up."

"That was nice of him. I hope it helped."

I nod. There was an awkward moment of silence until Jace took a deep breath and walked to the door.

"Get some rest okay, you have a long day ahead of you tomorrow."

He closed the door and I listened to his footsteps going down the hall. For some reason I feel nervous around him. _Why?_ But my thoughts were interrupted by a big yawn. _I guess I can get some rest. Who knows what I have to go through tomorrow._ Before I know it I am in a deep sleep plagued with terrible dreams.

 **Jace**

 _Why was Alec suddenly interested in helping Clary? Last time I checked he was mad at me for giving her a rune without even knowing if she was a Shadowhunter or not. I hadn't told her that there had been more demons than the ones we encountered at her house. If her mom could fight of demons she would have to have seraph blades; which she needs the rune of Angelic Power to hold. Clary most likely had Angel blood which she evidently does. But why does she suddenly show up now?_ Before I could ask any more questions someone knocks on my door. The door opens and Alec pops his head through. "Hey. Are you coming for training?"

"Yeah, in a sec, hold on."

"Ok see you in the training room."

I silently put my gear while letting my thoughts wander. _What's wrong with Alec?_ I wondered. _I mean he never acted like this before._ I walked out of the room on my way to train when I had an idea. _I should confront him about his change of heart. I mean it's not like he can hold a grudge against me forever. He's been weirdly happy all day except when he saw Clary. Something is wrong with-_

"Hey Jace!"

"Hey Alec! I have to ask you something." I started.

"Ok. Ask me anything you want!"

"Ok. Ummm… why are you so happy?"

"IHAVEABOYFRIEND. THATSRIGHT. IMGAYYYYYY AND I'M PROUD TO BE!"

Alec was talking a mile a minute and I couldn't understand what he was saying at all.

"Say that again SLOWER"

"Ok. Um… the high warlock of Brooklyn, Magnus Bane, is my boyfriend. I'm gay. It feels right. This is how I am meant to be. Don't tell anyone until I do, okay? You have to swear on the Angel, Jace."

"Ummmmm… Okay."

"Oh, come on Jace why can't you be happy for me?!"

"No sorry. I am happy for you but I'm a little shocked by your change of heart."

"Change of heart? What are you talking about/"

"Just yesterday you were mad at me for putting Clary in danger by putting a rune on her."

"Seriously, Jace. I was never mad at you. Well maybe a little but if you hadn't given her an iratze she could've died. You might have saved her life."

"Thanks. I could tell that her mom was a Shadowhunter. There was demon blood everywhere and there is only one thing that could have done that. There was still one left but it was slightly injured. It was the one that hurt Clary."

Alec stood wide-eyed. Then he took my arm, led me to a bench and said three words: "Tell me everything." so I did. I felt lighter when i had finished like always Alec listened nodding at the right parts. This is why he is my brother and my parabatai.

 **Who doesn't love a little Malec!**


End file.
